"It's a good time to transition," Ms. Swanson said, referring to her personal life (she has three school-age children) and that Mr. Emanuel is gearing up for a mayoral campaign and will want to have a new education chief in place. The mayor's office said a new adviser will be named soon.

Mr. Emanuel praised Ms. Swanson for her "knowledge and "good judgment" and for leading the charge in establishing numerous education programs in Chicago.

"Beth has led our team in improving public education from cradle through college," he said in a statement.

Ms. Swanson launched Chicago Summer of Learning, which provides formal and informal learning opportunities to children around the city. The program has been replicated in Los Angeles, Dallas, Pittsburgh, Washington, and Columbus, Ohio.

She also is credited with expanding early childhood education, longer school days for public school students and STEM, International Baccalaureate, charter and turnaround schools. Some of those programs have drawn criticism for coming at the expense of closures of some schools.

Before landing at City Hall, Ms. Swanson was executive director of the Pritzker Traubert Family Foundation, which supports programs for Chicago children. Prior to that she led the Chicago Public Schools Office of Management and Budget under then-CEO Arne Duncan.